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This code is based on the paper: "Inferring social network structure in ecological systems from spatio-temporal data streams" by Ioannis Psorakis, Stephen J. Roberts, Iead Rezek and Ben C. Sheldon, Journal of the Royal Society Interface, vol. 9 no. 76, pp 3055-3066 (2012). The following colleagues have also provided invaluable contributions, insights, bug reports and feature suggestions: Damien Farine Bernhard Voelkl Colin Garroway Reinder Radesma Lucy Aplin along with the rest of the Edward Grey Institute team at Oxford University Dept. of Zoology. ------ The package contains two scripts, run from the MATLAB command line: gmmevents.m: extracts gathering events and builds social network of statistically significant links gmmevents_groups_only.m: extracts ONLY the gathering events from the data stream The two scripts have different outputs and for more information please write on MATLAB prompt: >> help gmmevents %or >> help gmmevents_groups_only or see file description in the comments. Both scripts have a common input structure, which is: % INPUTS: % ------- % DATA: a Z-by-3 matrix, where Z the total number of observations. The % first column Z(:,1) denotes the real-valued timestamps of each observation. The % second column Z(:,2) denotes the indices of the individuals that were % recorded. Such indices must be INTEGER values, as they refer to nodes in % the adjacency matrix. Finally, the third column Z(:,3) denotes the index % of the location where the observation took place. Again, such indices % must be integer values. % Example: % % if we wish to see the contents of the 15th observation (z=15) in our % data stream, we write: % >> DATA(15,:) % ans = % 18516495 2 1 % % which reads: "the individual i=2 appeared at location l=1 at time % t=18516495" % % N: is the total number of distinct individuals in the data stream. If not % provided, it is automatically calculated by the second column of DATA % number_of_randomisations: the total number of data stream permutations % during link significance testing. If the user does not wish to perform % the test, set the value of that variable less or equal than 1, or not % pass it at all. --------
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Code for paper: Inferring social network structure in ecological systems from spatio-temporal data streams
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